bioRxiv Science⌕ Search

Biology subjects

Varma, V.

Publications and source records attributed to Varma, V..

11 recordsLinked to original sources
bioRxiv2024

De novo genome sequence assembly of the RNAi-tractable endosymbiosis model system Paramecium bursaria 186b reveals factors shaping intron repertoire

How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protist Paramecium bursaria hosts green algae of the order Chlorellales in a facultative photo-endosymbiosis. We have recently reported RNAi as a tool for understanding gene function in Paramecium bursaria 186b, CCAP strain 1660/18 [1]. To complement this work, here we report a highly complete host genome and transcriptome sequence dataset, using both Illumina and PacBio sequencing methods to aid genome analysis and to enable the design of RNAi experiments. Our analyses demonstrate Paramecium bursaria, like other ciliates such as diverse species of Paramecia, possess numerous tiny introns. These data, combined with the alternative genetic code common to ciliates, makes gene identification and annotation challenging. To explore intron evolutionary dynamics further we show that alternative splicing leading to intron retention occurs at a higher frequency among the smaller number of longer introns, identifying a source of selection against longer introns. These data will aid the investigation of genome evolution in the Paramecia and provide additional source data for the exploration of endosymbiotic functions.

genomics↗
bioRxiv2024

Sensitivities in associating land-system archetypes with sustainability metrics: Insights from simulations

Archetypes of land- and socio-ecological systems, generated using unsupervised classification methods, enable the assimilation of complex environmental and socio-economic information. Such simplification has considerable potential to feed into decision support systems for sustainability planning. But, the usefulness of archetypes depends on how well they relate to sustainability criteria, such as ecosystem service (ES) delivery, that are external to the input datasets employed for archetype generation. Sensitivities in such post-hoc association analyses, and the associated utility of the archetype framework in a decision support context, remain unexplored. Here we emulated post-hoc association analysis procedures using simulated socio-ecological datasets and ES response variables. Our simulations revealed a substantial influence on analysis performance from (1) the number of variables used as inputs in archetype generation, (2) the correlation structure of input datasets, (3) the type and distribution of input variables, and (4) the functional form (linear or non-linear) characterising the relationship between ES variables and their predictors. We observed near-identical performance when archetypes were generated using K-means clustering and Self-Organising Maps (SOMs) - two commonly used archetype classification methods. Further, better archetype classifier performance did not guarantee better discrimination of ES value distributions between archetypes. Our results suggest that designing a framework to generate archetypes for sustainability planning, and the selected methodological choices therein, should place greater emphasis on what the archetypes will be used for in downstream analyses, and not focus solely on archetype classifier performance. This would better ensure the identification of archetypes adaptable to a diverse array of sustainability indicators and sufficiently robust for monitoring decision outcomes over time.

ecology↗
bioRxiv2023

A model of sediment retention by vegetation for Great Britain: new methodologies & validation

Soil erosion is an substantial environmental concern worldwide. It has been historically and is of increasingly concern currently. Next to natural processes, over 2 million hectares of soil are at risk of erosion through intensifying agriculture in the Great Britain (England, Wales, Scotland and their territorial islands). Predictive soil erosion models, in the form of Ecosystem Service tools, aid in helping to identify areas that are vulnerable to soil erosion. Yet, no predictions for erosion or sediment retention by vegetation based on local data have been developed for Great Britain or the United Kingdom as a whole. Here we develop an erosion retention model using the InVEST platform, which is based on the RUSLE mathematical framework. We parameterise the model, as far as feasible, with GB specific input data. The developed model estimations are validated against suspended solids concentrations (sediments) in throughout England and Wales. Next to presenting the first GB wide estimate of erosion and erosion retention using the InVEST SDR module, we test three approaches here that differ from more widely applicable RUSLE model inputs, such as created for Europe as a whole. Here, we incorporate (1) periodicity to allow erosion to potentially fluctuate within years; (2) GB-specific cover periodic management factors estimates, including a range of crop types, based on observed satellite NDVI values (3) soil erosivity under heavy rainfall following GB estimates for 2000-2019. We conclude that both the GB created erosivity layer as the added periodicity do not seem to be provide substantial improvement over non-periodic estimated created with more widely available data, when validated against this set of suspended solids in rivers. In contrast, the observed cover management factors calculated from NDVI are a good improvement affecting the ranking order among catchments. Therefore, the generating of cover management factors using NDVI data could be promoted as method for InVEST SDR model development and in more general for developing RUSLE-based erosion estimates worldwide.

bioinformatics↗
bioRxiv2021

Captivity-induced behaviour and spatial learning abilities in an enigmatic, aquifer-dwelling blind eel, Rakthamichthys digressus

We investigated the impact of captive life on behaviour and learning abilities in an enigmatic, aquifer-dwelling blind eel, Rakthamichthys digressus. Of eight major behavioural traits related to exploration and activity in a novel arena, four were significantly altered by life in captivity. While the startle response upon introduction into the arena and overall swimming away from the walls increased after captivity, inactivity exhibited immediately after the startle and the reaction to an external disturbance decreased. We also observed behavioural syndromes between startle responses and horizontal wall following, and between overall activity and vertical wall following; however, these behavioural syndromes were not altered by maintenance in captivity. Interestingly, this blind-eel failed to learn a simple spatial task in a Y-maze apparatus. Captive-associated behavioural changes in R. digressus may influence their survival after reintroduction into natural habitats, and such changes must be taken into account while developing protocols for ex-situ conservation and subsequent release.

animal behavior and cognition↗
bioRxiv2020

Mapping the impacts of hurricanes Maria and Irma on banana production area in the Dominican Republic

Extreme weather events can have devastating impacts on agricultural systems, and the livelihoods that depend on them. Tools for rapid, comprehensive and cost-effective assessment of impacts, especially if carried out remotely, can be of great value in planning systematic recovery of production, as well as assessing risks from future events. Here, we use openly available remote sensing data to quantify the impacts of hurricanes Irma and Maria in 2017 on banana production area in the Dominican Republic -- the worlds largest producer of organic bananas. Further, we assess the risk to current production area if a similar extreme event were to re-occur. Hurricane associated damage was mapped using a simple change detection algorithm applied to Synthetic Aperture Radar (SAR) data over the three main banana growing provinces of northern Dominican Republic, i.e. Monte Cristi, Valverde and Santiago. The map of hurricane affected area was overlaid with banana plantation distributions for 2017 and 2019 that were mapped (accuracy = 99.8%) using a random forest classifier, and a combination of SAR and multi-spectral satellite data. Our results show that 11.35% of banana plantation area was affected by hurricane damage in 2017. Between 2017 and 2019, there was a high turnover of plantation area, but with a net gain of 10.8%. However, over a quarter (26.9%) of new plantation area spatially overlapped with regions which had seen flooding or damage from hurricanes in 2017. Our results indicate that banana production systems in northern Dominican Republic saw extensive damage in the aftermath of hurricanes Irma and Maria. While production area has recovered since then, a substantial proportion of new plantations, and a greater fraction of production area in general, occur at locations at risk from future extreme events.

ecology↗
bioRxiv2020

Social decision making is influenced by size of shoal but not personality or familiarity in Deccan Mahseer (Tor khudree)

Shoals formed by many piscine species are fission-fusion societies where decisions to leave or join a group can have consequences on the fitness of individuals. Some important factors that determine shoal choice are shoal size, familiarity and species composition. However, individuals and species often exhibit distinct shoaling preferences. Individual differences in shoaling preferences may also be related to personality traits such as boldness and sociability. In this study, we examined the link between shoaling decisions and personality traits in a hatchery reared population of an endangered megafish, the Deccan Mahseer (Tor khudree). We found that this fish exhibits a distinct preference for larger shoals at ratios of 1:2 or greater. However, they did not prefer to associate with an isolated familiar individual over unfamiliar ones or with a member of their own species over an invasive species. Moreover, shoaling preferences in individuals did not correlate with their boldness or sociability. These results suggest that hatchery reared mahseers which are reintroduced into natural habitats may shoal with invasive species, negatively affecting their viability. Modifying social behaviour of mahseers by amending rearing practices may be a useful strategy to improve outcomes of restocking interventions.

animal behavior and cognition↗
bioRxiv2019

Towards a Digital Diatom: image processing and deep learning analysis of Bacillaria paradoxa dynamic morphology

Recent years have witnessed a convergence of data and methods that allow us to approximate the shape, size, and functional attributes of biological organisms. This is not only limited to traditional model species: given the ability to culture and visualize a specific organism, we can capture both its structural and functional attributes. We present a quantitative model for the colonial diatom Bacillaria paradoxa, an organism that presents a number of unique attributes in terms of form and function. To acquire a digital model of B. paradoxa, we extract a series of quantitative parameters from microscopy videos from both primary and secondary sources. These data are then analyzed using a variety of techniques, including two rival deep learning approaches. We provide an overview of neural networks for non-specialists as well as present a series of analysis on Bacillaria phenotype data. The application of deep learning networks allows for two analytical purposes. Application of the DeepLabv3 pre-trained model extracts phenotypic parameters describing the shape of cells constituting Bacillaria colonies. Application of a semantic model trained on nematode embryogenesis data (OpenDevoCell) provides a means to analyze masked images of potential intracellular features. We also advance the analysis of Bacillaria colony movement dynamics by using templating techniques and biomechanical analysis to better understand the movement of individual cells relative to an entire colony. The broader implications of these results are presented, with an eye towards future applications to both hypothesis-driven studies and theoretical advancements in understanding the dynamic morphology of Bacillaria.

systems biology↗
bioRxiv2019

\"The Bold are the Sociable\": Personality, sociability and lateralized utilization of brain hemisphere in the juveniles of a megafish Deccan Mahseer (Tor khudree)

The present study explored relationships between personality traits; boldness, activity and sociability, and lateralized utilization of brain hemispheres in the hatchery reared juveniles of Deccan Mahseer (Tor khudree), a game fish inhabiting the rivers of central and southern India. Our results revealed a significant positive correlation between boldness and activity in this species when tested in isolation. However, boldness was positively correlated with the time spent near the individual conspecific but not with the individual alien invasive heterospecific tilapia (Oreochromis mossambicus). Although juvenile Deccan mahseer exhibited significant variation in the preference towards conspecific over heterospecific, no divergence in the utilization of right or left eye was seen while observing these individuals suggesting the lack of lateralized utilization of the brain hemispheres. Furthermore, laterality in visual preference failed to show any significant correlation with any of the personality traits tested in this species. Results are discussed in the light of the existing literature on the impact of life in homogenous hatchery conditions on the behaviour, personality traits and cognitive abilities of fishes.\n\nSignificance statementThe present study is one of the first that focuses on personality and lateralization in Deccan Mahseers, an endangered freshwater megafish. We report a positive linkage between boldness and sociability but do not find any correlation of personality with lateralized utilization of brain hemispheres in diverse social contexts. These findings have implications in the conservation and cultivation of this ecologically, culturally and economically important indigenous fish.

animal behavior and cognition↗
bioRxiv2018

Nutrient deposition enhances post-fire survival in non-N-fixing savanna tree seedlings

Nutrient deposition can modify plant growth rates and potentially alter the susceptibility of plants to disturbance events, while also influencing properties of disturbance regimes. In mixed tree-grass ecosystems, such as savannas and tropical dry forests, tree seedling growth rates strongly influence the ability of seedlings to survive fire (i.e. post-fire seedling survival), and hence, vegetation structure and tree community composition. However the effects of nutrient deposition on the susceptibility of recruiting trees to fire are poorly quantified. In a field experiment, seedlings of multiple N-fixing and non-N-fixing tropical dry forest tree species were exposed to nitrogen (N) and phosphorus (P) fertilisation, and fire. We quantified nutrient-mediated changes in a) mean seedling growth rates; b) growth rates of the fastest growing individuals and c) post-fire seedling survival. N-fixers had substantially higher baseline post-fire seedling survival, that was unaffected by nutrient addition. Fertilisation, especially with N, increased post-fire survival probabilities in non-N-fixers by increasing the growth rates of the fastest growing individuals. These results suggest that fertilisation can lead to an increase in the relative abundance of non-N-fixers in the resprout community, and thereby, alter the community composition of tropical savanna and dry forest tree communities in the long-term.

ecology↗
bioRxiv2017

Effects of increased N and P availability on biomass allocation and root carbohydrate reserves differ between N-fixing and non-N-fixing savanna tree seedlings

In mixed tree-grass ecosystems, tree recruitment is limited by demographic bottlenecks to seedling establishment arising from inter- and intra-life form competition, and disturbances such as fire. Enhanced nutrient availability resulting from anthropogenic nitrogen (N) and phosphorus (P) deposition can alter the nature of these bottlenecks by changing seedling growth and biomass allocation patterns, and lead to longer-term shifts in tree community composition if different plant functional groups respond differently to increased nutrient availability. However, the extent to which tree functional types characteristic of savannas differ in their responses to increased N and P availability remains unclear. We quantified differences in above- and belowground biomass, and root carbohydrate contents - parameters known to influence the ability of plants to compete, as well as survive and recover from fires - in seedlings of multiple N-fixing and non-N-fixing tree species characteristic of Indian savanna and dry-forest ecosystems to experimental N and P additions. N-fixers in our study were co-limited by N and P availability, while non-N-fixers were N limited. Although both functional groups increased biomass production following fertilisation, non-N-fixers were more responsive and showed greater relative increases in biomass with fertilisation than N-fixers. N-fixers had greater baseline investment in belowground resources and root carbohydrate stocks, and while fertilisation reduced root:shoot ratios in both functional groups, root carbohydrate content only reduced with fertilisation in non-N-fixers. Our results indicate that, even within a given system, plants belonging to different functional groups can be limited by, and respond differentially to, different nutrients, suggesting that long-term consequences of nutrient deposition are likely to vary across savannas contingent on the relative amounts of N and P being deposited in sites.

ecology↗